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Yeh SM, Yoon M, Scott S, Chatterjee A, Hemara LM, Chen RKY, Wang T, Templeton K, Rikkerink EHA, Jayaraman J, Brendolise C. NbPTR1 confers resistance against Pseudomonas syringae pv. actinidiae in kiwifruit. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38899426 DOI: 10.1111/pce.15002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) causes a devastating canker disease in yellow-fleshed kiwifruit (Actinidia chinensis). The effector HopZ5, which is present in all isolates of Psa3 causing global outbreaks of pandemic kiwifruit canker disease, triggers immunity in Nicotiana benthamiana and is not recognised in susceptible A. chinensis cultivars. In a search for N. benthamiana nonhost resistance genes against HopZ5, we found that the nucleotide-binding leucine-rich repeat receptor NbPTR1 recognised HopZ5. RPM1-interacting protein 4 orthologues from N. benthamiana and A. chinensis formed a complex with NbPTR1 and HopZ5 activity was able to disrupt this interaction. No functional orthologues of NbPTR1 were found in A. chinensis. NbPTR1 transformed into Psa3-susceptible A. chinensis var. chinensis 'Hort16A' plants introduced HopZ5-specific resistance against Psa3. Altogether, this study suggested that expressing NbPTR1 in Psa3-susceptible kiwifruit is a viable approach to acquiring resistance to Psa3 and it provides valuable information for engineering resistance in otherwise susceptible kiwifruit genotypes.
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Affiliation(s)
- Shin-Mei Yeh
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Minsoo Yoon
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Sidney Scott
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Abhishek Chatterjee
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Lauren M Hemara
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ronan K Y Chen
- Food Innovation, The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Tianchi Wang
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Kerry Templeton
- New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited (PFR), Motueka, New Zealand
| | - Erik H A Rikkerink
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Jay Jayaraman
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Cyril Brendolise
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
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2
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Sisson HM, Fagerlund RD, Jackson SA, Briers Y, Warring SL, Fineran PC. Antibacterial synergy between a phage endolysin and citric acid against the Gram-negative kiwifruit pathogen Pseudomonas syringae pv. actinidiae. Appl Environ Microbiol 2024; 90:e0184623. [PMID: 38319087 PMCID: PMC10952447 DOI: 10.1128/aem.01846-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
Horticultural diseases caused by bacterial pathogens provide an obstacle to crop production globally. Management of the infection of kiwifruit by the Gram-negative phytopathogen Pseudomonas syringae pv. actinidiae (Psa) currently includes copper and antibiotics. However, the emergence of bacterial resistance and a changing regulatory landscape are providing the impetus to develop environmentally sustainable antimicrobials. One potential strategy is the use of bacteriophage endolysins, which degrade peptidoglycan during normal phage replication, causing cell lysis and the release of new viral progeny. Exogenous use of endolysins as antimicrobials is impaired by the outer membrane of Gram-negative bacteria that provides an impermeable barrier and prevents endolysins from accessing their target peptidoglycan. Here, we describe the synergy between citric acid and a phage endolysin, which results in a reduction of viable Psa below detection. We show that citric acid drives the destabilization of the outer membrane via acidification and sequestration of divalent cations from the lipopolysaccharide, which is followed by the degradation of the peptidoglycan by the endolysin. Scanning electron microscopy revealed clear morphological differences, indicating cell lysis following the endolysin-citric acid treatment. These results show the potential for citric acid-endolysin combinations as a possible antimicrobial approach in agricultural applications. IMPORTANCE The phytopathogen Pseudomonas syringae pv. actinidiae (Psa) causes major impacts to kiwifruit horticulture, and the current control strategies are heavily reliant on copper and antibiotics. The environmental impact and increasing resistance to these agrichemicals are driving interest in alternative antimicrobials including bacteriophage-derived therapies. In this study, we characterize the endolysin from the Otagovirus Psa374 which infects Psa. When combined with citric acid, this endolysin displays an impressive antibacterial synergy to reduce viable Psa below the limit of detection. The use of citric acid as a synergistic agent with endolysins has not been extensively studied and has never been evaluated against a plant pathogen. We determined that the synergy involved a combination of the chelation activity of citric acid, acidic pH, and the specific activity of the ΦPsa374 endolysin. Our study highlights an exciting opportunity for alternative antimicrobials in agriculture.
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Affiliation(s)
- Hazel M. Sisson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
| | - Robert D. Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Simon A. Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Suzanne L. Warring
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Peter C. Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
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3
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Colombi E, Bertels F, Doulcier G, McConnell E, Pichugina T, Sohn KH, Straub C, McCann HC, Rainey PB. Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements. Proc Natl Acad Sci U S A 2024; 121:e2309263121. [PMID: 38457521 PMCID: PMC10945833 DOI: 10.1073/pnas.2309263121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 01/08/2024] [Indexed: 03/10/2024] Open
Abstract
Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness. Most ICEs characterized to date encode readily observable phenotypes contributing to symbiosis, pathogenicity, and antimicrobial resistance, yet the majority of ICEs carry genes of unknown function. Recent observations of rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements. Fifty-three unique ICE types were identified across the P. syringae species complex. Together they form a distinct family of ICEs (PsICEs) that share a distant relationship to ICEs found in Pseudomonas aeruginosa. PsICEs are defined by conserved backbone genes punctuated by an array of accessory cargo genes, are highly recombinogenic, and display distinct evolutionary histories compared to their bacterial hosts. The most common cargo is a recently disseminated 16-kb mobile genetic element designated Tn6212. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed fitness defects when grown on tricarboxylic acid (TCA) cycle intermediates. RNA-seq analysis of a set of nested deletion mutants showed that a Tn6212-encoded LysR regulator has global effects on chromosomal gene expression. We show that Tn6212 responds to preferred carbon sources and manipulates bacterial metabolism to maximize growth.
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Affiliation(s)
- Elena Colombi
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Guilhem Doulcier
- Laboratoire Biophysique et Évolution, Institut Chemie Biologie Innovation, École Supérieure de Physique et de Chemie Industrielles de la Ville de Paris, Université Paris Science et Lettres, Centre National de al Reserche Scientifique, Paris 75005, France
| | - Ellen McConnell
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Tatyana Pichugina
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Kee Hoon Sohn
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Christina Straub
- Health and Environment, Institute of Environmental Science and Research, Auckland 1025, New Zealand
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Honour C McCann
- Plant Pathogen Evolution Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Laboratoire Biophysique et Évolution, Institut Chemie Biologie Innovation, École Supérieure de Physique et de Chemie Industrielles de la Ville de Paris, Université Paris Science et Lettres, Centre National de al Reserche Scientifique, Paris 75005, France
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Wang H, Mi Q, Mao Y, Tan Y, Yang M, Liu W, Wang N, Tian X, Huang L. Streptothricin-F Inhibition of FtsZ Function: A Promising Approach for Controlling Pseudomonas syringae pv. actinidiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2624-2633. [PMID: 38277222 DOI: 10.1021/acs.jafc.3c08474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is a significant pathogenic bacterium affecting the kiwifruit industry. This study investigated the target sites of streptothricin-F (ST-F), produced by Streptomyces lavendulae gCLA4. The inhibition of ST-F on Psa was examined by the microscopic structural differences of Psa before and after treatment with ST-F, as well as the interaction between ST-F and cell division-related proteins. The results revealed filamentation of Psa after ST-F treatment, and fluorescence microscopy showed that ST-F inhibited the formation of the Z-ring composed of FtsZ protein. In vitro experiments and molecular docking demonstrated that ST-F can bind to FtsZ with a binding energy of 0.4 μM and inhibit FtsZ's GTP-dependent polymerization reaction. In addition, ST-F does not exert inhibitory effects on cell division in Psa strains overexpressing ftsZ. In conclusion, FtsZ is one of the target sites for ST-F inhibition of Psa, highlighting its potential as a therapeutic target for controlling Psa-induced kiwifruit bacterial canker.
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Affiliation(s)
- Hua Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100 Shaanxi Province, P. R. China
- College of Plant Protection, Northwest A&F University, Yangling Shaanxi Province 712100, P. R. China
| | - Qianqian Mi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100 Shaanxi Province, P. R. China
- College of Plant Protection, Northwest A&F University, Yangling Shaanxi Province 712100, P. R. China
| | - Yiru Mao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100 Shaanxi Province, P. R. China
- College of Plant Protection, Northwest A&F University, Yangling Shaanxi Province 712100, P. R. China
| | - Yunxiao Tan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100 Shaanxi Province, P. R. China
- College of Plant Protection, Northwest A&F University, Yangling Shaanxi Province 712100, P. R. China
| | - Mingming Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100 Shaanxi Province, P. R. China
- College of Plant Protection, Northwest A&F University, Yangling Shaanxi Province 712100, P. R. China
| | - Wei Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100 Shaanxi Province, P. R. China
- College of Plant Protection, Northwest A&F University, Yangling Shaanxi Province 712100, P. R. China
| | - Nana Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100 Shaanxi Province, P. R. China
- College of Life Science, Northwest A&F University, Yangling Shaanxi Province 712100, P. R. China
| | - Xiangrong Tian
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100 Shaanxi Province, P. R. China
- College of Forestry, Northwest A&F University, Yangling Shaanxi Province 712100, P. R. China
| | - Lili Huang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100 Shaanxi Province, P. R. China
- College of Plant Protection, Northwest A&F University, Yangling Shaanxi Province 712100, P. R. China
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5
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Santos MG, Nunes da Silva M, Vasconcelos MW, Carvalho SMP. Scientific and technological advances in the development of sustainable disease management tools: a case study on kiwifruit bacterial canker. FRONTIERS IN PLANT SCIENCE 2024; 14:1306420. [PMID: 38273947 PMCID: PMC10808555 DOI: 10.3389/fpls.2023.1306420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024]
Abstract
Plant disease outbreaks are increasing in a world facing climate change and globalized markets, representing a serious threat to food security. Kiwifruit Bacterial Canker (KBC), caused by the bacterium Pseudomonas syringae pv. actinidiae (Psa), was selected as a case study for being an example of a pandemic disease that severely impacted crop production, leading to huge economic losses, and for the effort that has been made to control this disease. This review provides an in-depth and critical analysis on the scientific progress made for developing alternative tools for sustainable KBC management. Their status in terms of technological maturity is discussed and a set of opportunities and threats are also presented. The gradual replacement of susceptible kiwifruit cultivars, with more tolerant ones, significantly reduced KBC incidence and was a major milestone for Psa containment - which highlights the importance of plant breeding. Nonetheless, this is a very laborious process. Moreover, the potential threat of Psa evolving to more virulent biovars, or resistant lineages to existing control methods, strengthens the need of keep on exploring effective and more environmentally friendly tools for KBC management. Currently, plant elicitors and beneficial fungi and bacteria are already being used in the field with some degree of success. Precision agriculture technologies, for improving early disease detection and preventing pathogen dispersal, are also being developed and optimized. These include hyperspectral technologies and forecast models for Psa risk assessment, with the latter being slightly more advanced in terms of technological maturity. Additionally, plant protection products based on innovative formulations with molecules with antibacterial activity against Psa (e.g., essential oils, phages and antimicrobial peptides) have been validated primarily in laboratory trials and with few compounds already reaching field application. The lessons learned with this pandemic disease, and the acquired scientific and technological knowledge, can be of importance for sustainably managing other plant diseases and handling future pandemic outbreaks.
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Affiliation(s)
- Miguel G. Santos
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
| | - Marta Nunes da Silva
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
- Universidade Católica Portuguesa, CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Marta W. Vasconcelos
- Universidade Católica Portuguesa, CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Susana M. P. Carvalho
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
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6
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Wang H, Wang N, Tan Y, Mi Q, Mao Y, Zhao C, Tian X, Liu W, Huang L. Paenibacillus polymyxa YLC1: a promising antagonistic strain for biocontrol of Pseudomonas syringae pv. actinidiae, causing kiwifruit bacterial canker. PEST MANAGEMENT SCIENCE 2023; 79:4357-4366. [PMID: 37417001 DOI: 10.1002/ps.7633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Kiwifruit bacterial canker (KBC) caused by Pseudomonas syringae pv. actinidiae (Psa) is the main limiting factor in the kiwifruit industry. This study aimed to identify bacterial strains with antagonistic activity against Psa, analyze antagonistically active substances and provide a new basis for the biological control of KBC. RESULTS A total of 142 microorganisms were isolated from the rhizosphere soil of asymptomatic kiwifruit. Among them, an antagonistic bacterial strain was identified as Paenibacillus polymyxa YLC1 by 16S rRNA sequencing. KBC control by strain YLC1 (85.4%) was comparable to copper hydroxide treatment (81.8%) under laboratory conditions and field testing. Active substances of strain YLC1 were identified by genetic sequence analysis using antiSMASH. Six biosynthetic active compound gene clusters were identified as encoding ester peptide synthesis, such as polymyxins. An active fraction was purified and identified as polymyxin B1 using chromatography, hydrogen nuclear magnetic resonance (NMR), and liquid chromatography-mass spectrometry. In addition, polymyxin B1 also was found significantly to suppress the expression of T3SS-related genes, but did not affect the growth of Psa at low concentrations. CONCLUSION In this study, a biocontrol strain P. polymyxa YLC1 obtained from kiwifruit rhizosphere soil exhibited excellent control effects on KBC in vitro and in field tests. Its active compound was identified as polymyxin B1, which inhibits a variety of pathogenic bacteria. We conclude that P. polymyxa YLC1 is a biocontrol strain with excellent prospects for development and application. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Hua Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Nana Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Yunxiao Tan
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Qianqian Mi
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Yiru Mao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Chao Zhao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Xiangrong Tian
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Forestry, Northwest A&F University, Yangling, People's Republic of China
| | - Wei Liu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Lili Huang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
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7
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Zhang Z, Long Y, Yin X, Wang W, Li W, Chen T, Chen J, Chen X, Wang B, Ma J. Metabolome and Transcriptome Analysis of Sulfur-Induced Kiwifruit Stem Laccase Gene Involved in Syringyl Lignin Synthesis against Bacterial Canker. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13566-13576. [PMID: 37651104 DOI: 10.1021/acs.jafc.3c02653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Kiwifruit canker is caused by Pseudomonas syringae pv. actinidiae and is one of the most destructive diseases of kiwifruit worldwide. Sulfur can improve the deposit of lignin in kiwifruit stems and induce disease resistance, but the action mechanism at the molecular level remains unclear. This omics-based study revealed that sulfur-induced S lignin synthesis contributes to disease resistance. Histological staining verified sulfur-enhanced total lignin deposition in kiwifruit stems. High-performance liquid chromatography and confocal Raman microscopy showed that sulfur-activated S lignin was mainly deposited in the cell corner. Metabolome and transcriptome analysis revealed that the levels of phenylpropanoid pathway S lignin precursors sinapic acid and sinapyl alcohol were significantly increased and 16 laccase genes were upregulated. Sulfur-induced resistance defense promoted elevated laccase activity by activating the laccase genes, participating in sinapic acid and sinapyl alcohol substance synthesis, and ultimately polymerizing S lignin at cell corner against kiwifruit canker disease.
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Affiliation(s)
- Zhuzhu Zhang
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Youhua Long
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
- Teaching Experiment Farm, Guizhou University, Guiyang 550025, China
| | - Xianhui Yin
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Weizhen Wang
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Wenzhi Li
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Tingting Chen
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Jia Chen
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xuetang Chen
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Bince Wang
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Jiling Ma
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
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8
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van Dijk B, Buffard P, Farr AD, Giersdorf F, Meijer J, Dutilh BE, Rainey PB. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome. ISME COMMUNICATIONS 2023; 3:90. [PMID: 37640834 PMCID: PMC10462680 DOI: 10.1038/s43705-023-00294-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.
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Affiliation(s)
- Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
| | - Pauline Buffard
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Andrew D Farr
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Franz Giersdorf
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL CNRS, Paris, France.
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9
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Wang B, Guo Y, Chen X, Ma J, Lei X, Wang W, Long Y. Assessment of the Biocontrol Potential of Bacillus velezensis WL-23 against Kiwifruit Canker Caused by Pseudomonas syringae pv. actinidiae. Int J Mol Sci 2023; 24:11541. [PMID: 37511299 PMCID: PMC10380555 DOI: 10.3390/ijms241411541] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Kiwifruit canker disease, caused by Pseudomonas syringae pv. actinidiae (Psa), is the main threat to kiwifruit production worldwide. Currently, there is no safe and effective disease prevention method; therefore, biological control technologies are being explored for Psa. In this study, Bacillus velezensis WL-23 was isolated from the leaf microbial community of kiwifruit and used to control kiwifruit cankers. Indoor confrontation experiments showed that both WL-23 and its aseptic filtrate had excellent inhibitory activity against the main fungal and bacterial pathogens of kiwifruit. Changes in OD600, relative conductivity, alkaline proteinase, and nucleic acid content were recorded during Psa growth after treatment with the aseptic filtrate, showing that Psa proliferation was inhibited and the integrity of the cell membrane was destroyed; this was further verified using scanning electron microscopy and transmission electron microscopy. In vivo, WL-23 promoted plant growth, increased plant antioxidant enzyme activity, and reduced canker incidence. Therefore, WL-23 is expected to become a biological control agent due to its great potential to contribute to sustainable agriculture.
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Affiliation(s)
- Bingce Wang
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Guizhou University, Guiyang 550025, China
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Yushan Guo
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Guizhou University, Guiyang 550025, China
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xuetang Chen
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Guizhou University, Guiyang 550025, China
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Jiling Ma
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Guizhou University, Guiyang 550025, China
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xia Lei
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Guizhou University, Guiyang 550025, China
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Weizhen Wang
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Guizhou University, Guiyang 550025, China
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Youhua Long
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Guizhou University, Guiyang 550025, China
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
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10
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Jiang H, Li C, Huang X, Ahmed T, Ogunyemi SO, Yu S, Wang X, Ali HM, Khan F, Yan C, Chen J, Li B. Phage combination alleviates bacterial leaf blight of rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1147351. [PMID: 37152174 PMCID: PMC10155274 DOI: 10.3389/fpls.2023.1147351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023]
Abstract
Rice bacterial leaf blight (BLB) is the most destructive bacterial diseases caused by Xanthomonas oryzae pv. oryzae (Xoo). Phages have been proposed as a green and efficient strategy to kill bacterial pathogens in crops, however, the mechanism of action of phages in the control of phyllosphere bacterial diseases remain unclear. Here, the glasshouse pot experiment results showed that phage combination could reduce the disease index by up to 64.3%. High-throughput sequencing technology was used to analyze the characteristics of phyllosphere microbiome changes and the results showed that phage combinations restored the impact of pathogen invasion on phyllosphere communities to a certain extent, and increased the diversity of bacterial communities. In addition, the phage combination reduced the relative abundance of epiphytic and endophytic Xoo by 58.9% and 33.9%, respectively. In particular, Sphingomonas and Stenotrophomonas were more abundant. According to structural equation modeling, phage combination directly and indirectly affected the disease index by affecting pathogen Xoo biomass and phage resistance. In summary, phage combination could better decrease the disease index. These findings provide new insights into phage biological control of phyllosphere bacterial diseases, theoretical data support, and new ideas for agricultural green prevention and control of phyllosphere diseases.
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Affiliation(s)
- Hubiao Jiang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Changxin Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Xuefang Huang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shanhong Yu
- Taizhou Academy of Agricultural Sciences, Taizhou, China
| | - Xiao Wang
- Ningbo Jiangbei District Agricultural Technology Extension Service Station, Ningbo, China
| | - Hayssam M. Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fahad Khan
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS, Australia
| | - Chengqi Yan
- Institute of Biotechnology, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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11
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Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes. Antibiotics (Basel) 2023; 12:antibiotics12020333. [PMID: 36830244 PMCID: PMC9952537 DOI: 10.3390/antibiotics12020333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.
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12
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Fiorillo A, Frezza D, Di Lallo G, Visconti S. A Phage Therapy Model for the Prevention of Pseudomonas syringae pv. actinidiae Infection of Kiwifruit Plants. PLANT DISEASE 2023; 107:267-271. [PMID: 35939740 DOI: 10.1094/pdis-02-22-0348-sc] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Great efforts have been made with chemicals and pesticides to contain the spread of Pseudomonas syringae pv. actinidiae (Psa) responsible for kiwifruit canker. Unfortunately, only partial results were obtained for this bacterial pandemic, and alternative remedies were proposed to avoid soil pollution and the onset of antibiotic resistance. Among these, phage therapy represents a possible tool with low environmental impact and high specificity. Several phages have been isolated and tested for the capacity to kill Psa in vitro, but experiments to verify their efficacy in vivo are still lacking. In the present study, we demonstrated that the phage φPSA2 (previously characterized) contains the spread of Psa inside plant tissue and reduces the symptoms of the disease. Our data are a strong indication for the efficiency of this phage and open the possibility of developing a phage therapy based on φPSA2 to counteract the bacterial canker of kiwifruit.
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Affiliation(s)
- Anna Fiorillo
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Domenico Frezza
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Gustavo Di Lallo
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Sabina Visconti
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
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13
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Luo J, Dai D, Lv L, Ahmed T, Chen L, Wang Y, An Q, Sun G, Li B. Advancements in the Use of Bacteriophages to Combat the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae. Viruses 2022; 14:2704. [PMID: 36560706 PMCID: PMC9785728 DOI: 10.3390/v14122704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Over the last several decades, kiwifruit production has been severely damaged by the bacterial plant pathogen Pseudomonas syringae pv. actinidiae (Psa), resulting in severe economic losses worldwide. Currently, copper bactericides and antibiotics are the main tools used to control this bacterial disease. However, their use is becoming increasingly ineffective due to the emergence of antibiotic resistance. In addition, environmental issues and the changes in the composition of soil bacterial communities are also concerning when using these substances. Although biocontrol methods have shown promising antibacterial effects on Psa infection under in vitro conditions, the efficiency of antagonistic bacteria and fungi when deployed under field conditions remains unclear. Therefore, it is crucial to develop a phage-based biocontrol strategy for this bacterial pathogen. Due to the specificity of the target bacteria and for the benefit of the environment, bacteriophages (phages) have been widely regarded as promising biological agents to control plant, animal, and human bacterial diseases. An increasing number of studies focus on the use of phages for the control of plant diseases, including the kiwifruit bacterial canker. In this review, we first introduce the characteristics of the Psa-induced kiwifruit canker, followed by a description of the diversity and virulence of Psa strains. The main focus of the review is the description of recent advances in the isolation of Psa phages and their characterization, including morphology, host range, lytic activity, genome characterization, and lysis mechanism, but we also describe the biocontrol strategies together with potential challenges introduced by abiotic factors, such as high temperature, extreme pH, and UV irradiation in kiwifruit orchards. The information presented in this review highlights the potential role of phages in controlling Psa infection to ensure plant protection.
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Affiliation(s)
- Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Dejiang Dai
- Station for the Plant Protection & Quarantine and Control of Agrochemicals Zhejiang Province, Hangzhou 310004, China
| | - Luqiong Lv
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lei Chen
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Yanli Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qianli An
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guochang Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Bin Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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14
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Gonçalves OS, de Assis JCS, Santana MF. Breaking the ICE: an easy workflow for identifying and analyzing integrative and conjugative elements in bacterial genomes. Funct Integr Genomics 2022; 22:1139-1145. [PMID: 36149586 DOI: 10.1007/s10142-022-00903-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/18/2023]
Affiliation(s)
- Osiel Silva Gonçalves
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Jessica Catarine Silva de Assis
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Mateus Ferreira Santana
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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15
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Yoon M, Middleditch MJ, Rikkerink EHA. A conserved glutamate residue in RPM1-INTERACTING PROTEIN4 is ADP-ribosylated by the Pseudomonas effector AvrRpm2 to activate RPM1-mediated plant resistance. THE PLANT CELL 2022; 34:4950-4972. [PMID: 36130293 PMCID: PMC9710000 DOI: 10.1093/plcell/koac286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Gram-negative bacterial plant pathogens inject effectors into their hosts to hijack and manipulate metabolism, eluding surveillance at the battle frontier on the cell surface. The effector AvrRpm1Pma from Pseudomonas syringae pv. maculicola functions as an ADP-ribosyl transferase that modifies RESISTANCE TO P. SYRINGAE PV MACULICOLA1 (RPM1)-INTERACTING PROTEIN4 (RIN4), leading to the activation of Arabidopsis thaliana (Arabidopsis) resistance protein RPM1. Here we confirmed the ADP-ribosyl transferase activity of another bacterial effector, AvrRpm2Psa from P. syringae pv. actinidiae, via sequential inoculation of Pseudomonas strain Pto DC3000 harboring avrRpm2Psa following Agrobacterium-mediated transient expression of RIN4 in Nicotiana benthamiana. We conducted mutational analysis in combination with mass spectrometry to locate the target site in RIN4. A conserved glutamate residue (Glu156) is the most likely target for AvrRpm2Psa, as only Glu156 could be ADP-ribosylated to activate RPM1 among candidate target residues identified from the MS/MS fragmentation spectra. Soybean (Glycine max) and snap bean (Phaseolus vulgaris) RIN4 homologs without glutamate at the positions corresponding to Glu156 of Arabidopsis RIN4 are not ADP-ribosylated by bacterial AvrRpm2Psa. In contrast to the effector AvrB, AvrRpm2Psa does not require the phosphorylation of Thr166 in RIN4 to activate RPM1. Therefore, separate biochemical reactions by different pathogen effectors may trigger the activation of the same resistance protein via distinct modifications of RIN4.
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Affiliation(s)
- Minsoo Yoon
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Martin J Middleditch
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Erik H A Rikkerink
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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16
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Correia C, Magnani F, Pastore C, Cellini A, Donati I, Pennisi G, Paucek I, Orsini F, Vandelle E, Santos C, Spinelli F. Red and Blue Light Differently Influence Actinidia chinensis Performance and Its Interaction with Pseudomonas syringae pv. Actinidiae. Int J Mol Sci 2022; 23:13145. [PMID: 36361938 PMCID: PMC9658526 DOI: 10.3390/ijms232113145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 03/08/2024] Open
Abstract
Light composition modulates plant growth and defenses, thus influencing plant-pathogen interactions. We investigated the effects of different light-emitting diode (LED) red (R) (665 nm) and blue (B) (470 nm) light combinations on Actinidia chinensis performance by evaluating biometric parameters, chlorophyll a fluorescence, gas exchange and photosynthesis-related gene expression. Moreover, the influence of light on the infection by Pseudomonas syringae pv. actinidiae (Psa), the etiological agent of bacterial canker of kiwifruit, was investigated. Our study shows that 50%R-50%B (50R) and 25%R-75%B (25R) lead to the highest PSII efficiency and photosynthetic rate, but are the least effective in controlling the endophytic colonization of the host by Psa. Monochromatic red light severely reduced ΦPSII, ETR, Pn, TSS and photosynthesis-related genes expression, and both monochromatic lights lead to a reduction of DW and pigments content. Monochromatic blue light was the only treatment significantly reducing disease symptoms but did not reduce bacterial endophytic population. Our results suggest that monochromatic blue light reduces infection primarily by modulating Psa virulence more than host plant defenses.
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Affiliation(s)
- Cristiana Correia
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
- IB2Lab, LAQV-Requimte, Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Federico Magnani
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Chiara Pastore
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Antonio Cellini
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Irene Donati
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Pennisi
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Ivan Paucek
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Francesco Orsini
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Elodie Vandelle
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Conceição Santos
- IB2Lab, LAQV-Requimte, Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Francesco Spinelli
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
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17
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Warring SL, Malone LM, Jayaraman J, Easingwood RA, Rigano LA, Frampton RA, Visnovsky SB, Addison SM, Hernandez L, Pitman AR, Lopez Acedo E, Kleffmann T, Templeton MD, Bostina M, Fineran PC. A lipopolysaccharide-dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance. Environ Microbiol 2022; 24:4834-4852. [PMID: 35912527 PMCID: PMC9796965 DOI: 10.1111/1462-2920.16106] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
Bacterial pathogens are major causes of crop diseases, leading to significant production losses. For instance, kiwifruit canker, caused by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), has posed a global challenge to kiwifruit production. Treatment with copper and antibiotics, whilst initially effective, is leading to the rise of bacterial resistance, requiring new biocontrol approaches. Previously, we isolated a group of closely related Psa phages with biocontrol potential, which represent environmentally sustainable antimicrobials. However, their deployment as antimicrobials requires further insight into their properties and infection strategy. Here, we provide an in-depth examination of the genome of ΦPsa374-like phages and show that they use lipopolysaccharides (LPS) as their main receptor. Through proteomics and cryo-electron microscopy of ΦPsa374, we revealed the structural proteome and that this phage possess a T = 9 capsid triangulation, unusual for myoviruses. Furthermore, we show that ΦPsa374 phage resistance arises in planta through mutations in a glycosyltransferase involved in LPS synthesis. Lastly, through in vitro evolution experiments we showed that phage resistance is overcome by mutations in a tail fibre and structural protein of unknown function in ΦPsa374. This study provides new insight into the properties of ΦPsa374-like phages that informs their use as antimicrobials against Psa.
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Affiliation(s)
- Suzanne L. Warring
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Lucia M. Malone
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Jay Jayaraman
- The New Zealand Institute for Plant & Food Research Limited, Mt AlbertAucklandNew Zealand,Bioprotection AotearoaCanterburyNew Zealand
| | | | - Luciano A. Rigano
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Plant Health & Environment Laboratory, Biosecurity New ZealandMinistry for Primary IndustriesAucklandNew Zealand
| | - Rebekah A. Frampton
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Sandra B. Visnovsky
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Shea M. Addison
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Loreto Hernandez
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Andrew R. Pitman
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand,Foundation for Arable Research (FAR), TempletonChristchurchNew Zealand
| | - Elena Lopez Acedo
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | | | - Matthew D. Templeton
- The New Zealand Institute for Plant & Food Research Limited, Mt AlbertAucklandNew Zealand,Bioprotection AotearoaCanterburyNew Zealand,School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Mihnea Bostina
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Otago Centre for Electron MicroscopyUniversity of OtagoDunedinNew Zealand
| | - Peter C. Fineran
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Bioprotection AotearoaCanterburyNew Zealand
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18
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Yu JJ, Wei WK, Zhang Y, Cox RJ, He J, Liu JK, Feng T. Terpenoids from Kiwi endophytic fungus Bipolaris sp. and their antibacterial activity against Pseudomonas syringae pv. actinidiae. Front Chem 2022; 10:990734. [PMID: 36118317 PMCID: PMC9475172 DOI: 10.3389/fchem.2022.990734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
A chemical investigation on the kiwi endophytic fungus Bipolaris sp. Resulted in the isolation of eight new terpenoids (1–8) and five known analogues (9–13). Compounds 1–5 are novel sativene sesquiterpenoids containing three additional skeletal carbons, while compounds 4 and 5 are rare dimers. Compounds 6–8 and 13 are sesterterpenoids that have been identified from this species for the first time. Compounds 4 and 5 showed antibacterial activity against kiwifruit canker pathogen Pseudomonas syringae pv. Actinidiae (Psa) with MIC values of 32 and 64 μg/ml, respectively.
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Affiliation(s)
- Jun-Jie Yu
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Wen-Ke Wei
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Yu Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Russell J. Cox
- Institute for Organic Chemistry and Biomolekulares Wirkstoffzentrum (BMWZ), Hannover, Germany
| | - Juan He
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
- *Correspondence: Juan He, ; Ji-Kai Liu, ; Tao Feng,
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
- *Correspondence: Juan He, ; Ji-Kai Liu, ; Tao Feng,
| | - Tao Feng
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
- *Correspondence: Juan He, ; Ji-Kai Liu, ; Tao Feng,
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19
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Genomic Variation and Host Interaction among Pseudomonas syringae pv. actinidiae Strains in Actinidia chinensis ‘Hongyang’. Int J Mol Sci 2022; 23:ijms23179743. [PMID: 36077140 PMCID: PMC9456109 DOI: 10.3390/ijms23179743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Kiwifruit bacterial canker is a recent epidemic disease caused by Pseudomonas syringae pv. actinidiae (Psa), which has undergone worldwide expansion in a short time and resulted in significant economic losses. ‘Hongyang’ (Actinidia chinensis), a widely grown cultivar because of its health-beneficial nutrients and appreciated red-centered inner pericarp, is highly sensitive to Psa. In this work, ten Psa strains were isolated from ‘Hongyang’ and sequenced for genome analysis. The results indicated divergences in pathogenicity and pathogenic-related genes among the Psa strains. Significantly, the interruption at the 596 bp of HrpR in two low-pathogenicity strains reemphasized this gene, expressing a transcriptional regulator for the effector secretion system, as an important pathogenicity-associated locus of Psa. The transcriptome analysis of ‘Hongyang’ infected with different Psa strains was performed by RNA-seq of stem tissues locally (at the inoculation site) and systemically. Psa infection re-programmed the host genes expression, and the susceptibility to Psa might be attributed to the down-regulation of several genes involved in plant-pathogen interactions, especially calcium signaling transduction, as well as fatty acid elongation. This suppression was found in both low- and high-pathogenicity Psa inoculated tissues, but the effect was stronger with more virulent strains. Taken together, the divergences of P. syringae pv. actinidiae in pathogenicity, genome, and resulting transcriptomic response of A. chinensis provide insights into unraveling the molecular mechanism of Psa-kiwifruit interactions and resistance improvement in the kiwifruit crop.
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Sharma A, Abrahamian P, Carvalho R, Choudhary M, Paret ML, Vallad GE, Jones JB. Future of Bacterial Disease Management in Crop Production. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:259-282. [PMID: 35790244 DOI: 10.1146/annurev-phyto-021621-121806] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial diseases are a constant threat to crop production globally. Current management strategies rely on an array of tactics, including improved cultural practices; application of bactericides, plant activators, and biocontrol agents; and use of resistant varieties when available. However, effective management remains a challenge, as the longevity of deployed tactics is threatened by constantly changing bacterial populations. Increased scrutiny of the impact of pesticides on human and environmental health underscores the need for alternative solutions that are durable, sustainable, accessible to farmers, and environmentally friendly. In this review, we discuss the strengths and shortcomings of existing practices and dissect recent advances that may shape the future of bacterial disease management. We conclude that disease resistance through genome modification may be the most effective arsenal against bacterial diseases. Nonetheless, more research is necessary for developing novel bacterial disease management tactics to meet the food demand of a growing global population.
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Affiliation(s)
- Anuj Sharma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
| | - Peter Abrahamian
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
- Plant Pathogen Confirmatory Diagnostic Laboratory, USDA-APHIS, Beltsville, Maryland, USA
| | - Renato Carvalho
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
| | - Manoj Choudhary
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
| | - Mathews L Paret
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
- North Florida Research and Education Center, University of Florida, Quincy, Florida, USA
| | - Gary E Vallad
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
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21
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Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria. Mob DNA 2022; 13:19. [PMID: 35962419 PMCID: PMC9373382 DOI: 10.1186/s13100-022-00275-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/22/2022] [Indexed: 11/29/2022] Open
Abstract
Background ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact. Results Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants. Conclusions Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00275-1.
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Mariz-Ponte N, Gimranov E, Rego R, Moura L, Santos C, Tavares F. Distinct phenotypic behaviours within a clonal population of Pseudomonas syringae pv. actinidiae. PLoS One 2022; 17:e0269343. [PMID: 35679321 PMCID: PMC9182710 DOI: 10.1371/journal.pone.0269343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/18/2022] [Indexed: 11/18/2022] Open
Abstract
Bacterial canker of the kiwifruit caused by the etiological agent Pseudomonas syringae pv. actinidiae is the most severe disease in kiwifruit production. Since 2008 a hypervirulent Psa biovar 3 has spread rapidly worldwide. Different genomic and phenotypic approaches have been used to understand the origin of the dissemination and geographical evolution of populations associated with this pandemic. This study aimed to characterize the genetic and phenotypic diversity of 22 Psa isolates collected in different regions of Portugal between 2013 and 2017. Genotypic and phenotypic characterization was based on Multi-Locus Sequence Analysis (MLSA), motility, IAA production, Biolog GEN III, and copper sensitivity. No polymorphisms were detected for the concatenated sequence (1950 bp) of the housekeeping genes gltA, gapA, gyrB, and rpoD. Results support the analysed Portuguese Psa isolates (2013–2017) belonging to Psa3, and MLSA indicates high genetic clonality and stability of these populations. The phenotypic analysis through Biolog revealed a heterogeneous pattern in the Psa collection and its position in the Pseudomonas complex. This heterogeneity reflects a genomic diversity that may reflect distinct adaptive trends associated with the environmental conditions and widespread. The Portuguese Psa collection showed no resistance to copper. This information is relevant to kiwi producers that predominantly use Cu-treatments to control kiwifruit bacterial canker.
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Affiliation(s)
- Nuno Mariz-Ponte
- Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- LAQV-REQUIMTE, Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- CIBIO-Research Centre in Biodiversity and Genetic Resources, In-BIO-Associate Laboratory, Campus de Vairão, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- * E-mail:
| | - Emil Gimranov
- Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- LAQV-REQUIMTE, Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
| | - Rute Rego
- CISAS—Centre for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Luísa Moura
- CISAS—Centre for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Conceição Santos
- Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- LAQV-REQUIMTE, Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
| | - Fernando Tavares
- Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- CIBIO-Research Centre in Biodiversity and Genetic Resources, In-BIO-Associate Laboratory, Campus de Vairão, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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Hemara LM, Jayaraman J, Sutherland PW, Montefiori M, Arshed S, Chatterjee A, Chen R, Andersen MT, Mesarich CH, van der Linden O, Yoon M, Schipper MM, Vanneste JL, Brendolise C, Templeton MD. Effector loss drives adaptation of Pseudomonas syringae pv. actinidiae biovar 3 to Actinidia arguta. PLoS Pathog 2022; 18:e1010542. [PMID: 35622878 PMCID: PMC9182610 DOI: 10.1371/journal.ppat.1010542] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 06/09/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022] Open
Abstract
A pandemic isolate of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) has devastated kiwifruit orchards growing cultivars of Actinidia chinensis. In contrast, A. arguta (kiwiberry) is not a host of Psa3. Resistance is mediated via effector-triggered immunity, as demonstrated by induction of the hypersensitive response in infected A. arguta leaves, observed by microscopy and quantified by ion-leakage assays. Isolates of Psa3 that cause disease in A. arguta have been isolated and analyzed, revealing a 51 kb deletion in the exchangeable effector locus (EEL). This natural EEL-mutant isolate and strains with synthetic knockouts of the EEL were more virulent in A. arguta plantlets than wild-type Psa3. Screening of a complete library of Psa3 effector knockout strains identified increased growth in planta for knockouts of four effectors–AvrRpm1a, HopF1c, HopZ5a, and the EEL effector HopAW1a –suggesting a resistance response in A. arguta. Hypersensitive response (HR) assays indicate that three of these effectors trigger a host species-specific HR. A Psa3 strain with all four effectors knocked out escaped host recognition, but a cumulative increase in bacterial pathogenicity and virulence was not observed. These avirulence effectors can be used in turn to identify the first cognate resistance genes in Actinidia for breeding durable resistance into future kiwifruit cultivars. Clonally propagated monoculture crop plants facilitate the emergence and spread of new diseases. Plant pathogens cause disease by the secretion of effectors that function by repressing the host defense response. While the last few decades have seen a huge increase in our understanding of the role effectors play in mediating plant-pathogen interactions, the combinations of effectors required for the establishment of plant disease and that account for host specificity are less well understood. Breeding genetic resistance is often used to protect plants from disease but it is frequently evaded by rapidly evolving pathogens. Pseudomonas syringae pv. actinidiae (Psa) which causes bacterial canker disease of kiwifruit has spread rapidly throughout the world’s kiwifruit orchards, particularly those growing cultivars of Actinidia chinensis. Other Actinidia species including A. arguta display strong resistance conferred by recognition of effectors delivered by Psa. We explore the depth and dynamics of Psa effector recognition by A. arguta and show that there is a trade-off between losses of effector recognition by A. arguta versus the retention of pathogenicity. Our findings should aid in the understanding of how to breed durable resistance into perennial plants challenged by swiftly evolving pathogens.
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Affiliation(s)
- Lauren M. Hemara
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Bioprotection Aoteoroa, New Zealand
| | - Jay Jayaraman
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
- Bioprotection Aoteoroa, New Zealand
| | - Paul W. Sutherland
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Mirco Montefiori
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Saadiah Arshed
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Abhishek Chatterjee
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Ronan Chen
- The New Zealand Institute for Plant and Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Mark T. Andersen
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Carl H. Mesarich
- Bioprotection Aoteoroa, New Zealand
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Otto van der Linden
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Minsoo Yoon
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Magan M. Schipper
- The New Zealand Institute for Plant and Food Research Limited, Ruakura Campus, Hamilton, New Zealand
| | - Joel L. Vanneste
- The New Zealand Institute for Plant and Food Research Limited, Ruakura Campus, Hamilton, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Bioprotection Aoteoroa, New Zealand
- * E-mail: ,
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Host-specific signal perception by PsaR2 LuxR solo induces Pseudomonas syringae pv. actinidiae virulence traits. Microbiol Res 2022; 260:127048. [DOI: 10.1016/j.micres.2022.127048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/23/2022] [Accepted: 04/19/2022] [Indexed: 11/19/2022]
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Baltrus DA, Feng Q, Kvitko BH. Genome Context Influences Evolutionary Flexibility of Nearly Identical Type III Effectors in Two Phytopathogenic Pseudomonads. Front Microbiol 2022; 13:826365. [PMID: 35250942 PMCID: PMC8895235 DOI: 10.3389/fmicb.2022.826365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 12/02/2022] Open
Abstract
Integrative Conjugative Elements (ICEs) are replicons that can insert and excise from chromosomal locations in a site-specific manner, can conjugate across strains, and which often carry a variety of genes useful for bacterial growth and survival under specific conditions. Although ICEs have been identified and vetted within certain clades of the agricultural pathogen Pseudomonas syringae, the impact of ICE carriage and transfer across the entire P. syringae species complex remains underexplored. Here we identify and vet an ICE (PmaICE-DQ) from P. syringae pv. maculicola ES4326, a strain commonly used for laboratory virulence experiments, demonstrate that this element can excise and conjugate across strains, and highlight that this element contains loci encoding multiple type III effector proteins. Moreover, genome context suggests that another ICE (PmaICE-AOAB) is highly similar in comparison with and found immediately adjacent to PmaICE-DQ within the chromosome of strain ES4326, and also contains multiple type III effectors. Lastly, we present passage data from in planta experiments that suggests that genomic plasticity associated with ICEs may enable strains to more rapidly lose type III effectors that trigger R-gene mediated resistance in comparison to strains where nearly isogenic effectors are not present in active ICEs. Taken together, our study sheds light on a set of ICE elements from P. syringae pv. maculicola ES4326 and suggests how genomic context may lead to different evolutionary dynamics for shared virulence genes between strains.
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Affiliation(s)
- David A. Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
- *Correspondence: David A. Baltrus,
| | - Qian Feng
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
- Brian H. Kvitko,
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de Souza-Neto RR, Carvalho IGB, Martins PMM, Picchi SC, Tomaz JP, Caserta R, Takita MA, de Souza AA. MqsR toxin as a biotechnological tool for plant pathogen bacterial control. Sci Rep 2022; 12:2794. [PMID: 35181693 PMCID: PMC8857320 DOI: 10.1038/s41598-022-06690-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/23/2021] [Indexed: 11/09/2022] Open
Abstract
Type II toxin-antitoxin (TA) systems are widespread in bacteria and are involved in important cell features, such as cell growth inhibition and antimicrobial tolerance, through the induction of persister cells. Overall, these characteristics are associated with bacterial survival under stress conditions and represent a significant genetic mechanism to be explored for antibacterial molecules. We verified that even though Xylella fastidiosa and Xanthomonas citri subsp. citri share closely related genomes, they have different Type II TA system contents. One important difference is the absence of mqsRA in X. citri. The toxin component of this TA system has been shown to inhibit the growth of X. fastidiosa. Thus, the absence of mqsRA in X. citri led us to explore the possibility of using the MqsR toxin to impair X. citri growth. We purified MqsR and confirmed that the toxin was able to inhibit X. citri. Subsequently, transgenic citrus plants producing MqsR showed a significant reduction in citrus canker and citrus variegated chlorosis symptoms caused, respectively, by X. citri and X. fastidiosa. This study demonstrates that the use of toxins from TA systems is a promising strategy to be explored aiming bacterial control.
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Affiliation(s)
- Reinaldo Rodrigues de Souza-Neto
- Citrus Research Center, Agronomic Institute - IAC, Cordeirópolis, SP, Brazil.,Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | | | | | | | - Juarez Pires Tomaz
- Rural Development Institute of Parana - IAPAR-EMATER, Londrina, PR, Brazil
| | - Raquel Caserta
- Citrus Research Center, Agronomic Institute - IAC, Cordeirópolis, SP, Brazil
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A large transposable element mediates metal resistance in the fungus Paecilomyces variotii. Curr Biol 2022; 32:937-950.e5. [PMID: 35063120 DOI: 10.1016/j.cub.2021.12.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/11/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022]
Abstract
The horizontal transfer of large gene clusters by mobile elements is a key driver of prokaryotic adaptation in response to environmental stresses. Eukaryotic microbes face similar stresses; however, a parallel role for mobile elements has not been established. A stress faced by many microorganisms is toxic metal ions in their environment. In fungi, identified mechanisms for protection against metals generally rely on genes that are dispersed within an organism's genome. Here, we discover a large (∼85 kb) region that confers tolerance to five metal/metalloid ions (arsenate, cadmium, copper, lead, and zinc) in the genomes of some, but not all, strains of a fungus, Paecilomyces variotii. We name this region HEPHAESTUS (Hφ) and present evidence that it is mobile within the P. variotii genome with features characteristic of a transposable element. HEPHAESTUS contains the greatest complement of host-beneficial genes carried by a transposable element in eukaryotes, suggesting that eukaryotic transposable elements might play a role analogous to bacteria in the horizontal transfer of large regions of host-beneficial DNA. Genes within HEPHAESTUS responsible for individual metal tolerances include those encoding a P-type ATPase transporter-PcaA-required for cadmium and lead tolerance, a transporter-ZrcA-providing tolerance to zinc, and a multicopper oxidase-McoA-conferring tolerance to copper. In addition, a subregion of Hφ confers tolerance to arsenate. The genome sequences of other fungi in the Eurotiales contain further examples of HEPHAESTUS, suggesting that it is responsible for independently assembling tolerance to a diverse array of ions, including chromium, mercury, and sodium.
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Yu JJ, Jin YX, Huang SS, He J. Sesquiterpenoids and Xanthones from the Kiwifruit-Associated Fungus Bipolaris sp. and Their Anti-Pathogenic Microorganism Activity. J Fungi (Basel) 2021; 8:9. [PMID: 35049949 PMCID: PMC8781276 DOI: 10.3390/jof8010009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
Nine previously undescribed sesquiterpenoids, bipolarisorokins A-I (1-9); two new xanthones, bipolarithones A and B (10 and 11); two novel sativene-xanthone adducts, bipolarithones C and D (12 and 13); as well as five known compounds (14-18) were characterized from the kiwifruit-associated fungus Bipolaris sp. Their structures were elucidated by extensive spectroscopic methods, electronic circular dichroism (ECD), 13C NMR calculations, DP4+ probability analyses, and single crystal X-ray diffractions. Many compounds exhibited anti-pathogenic microorganism activity against the bacterium Pseudomonas syringae pv. actinidiae and four pathogenic microorganisms.
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Affiliation(s)
| | | | | | - Juan He
- National Demonstration Center for Experimental Ethnopharmacology Education, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China; (J.-J.Y.); (Y.-X.J.); (S.-S.H.)
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29
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Martino G, Holtappels D, Vallino M, Chiapello M, Turina M, Lavigne R, Wagemans J, Ciuffo M. Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy. Viruses 2021; 13:2083. [PMID: 34696512 PMCID: PMC8537276 DOI: 10.3390/v13102083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial kiwifruit vine disease (Pseudomonas syringae pv. actinidiae, Psa) and halo blight of bean (P. syringae pv. phaseolicola, Pph) are routinely treated with copper, leading to environmental pollution and bacterial copper resistance. An alternative sustainable control method could be based on bacteriophages, as phage biocontrol offers high specificity and does not result in the spread of toxic residues into the environment or the food chain. In this research, specific phages suitable for phage-based biocontrol strategies effective against Psa and Pph were isolated and characterized. In total, sixteen lytic Pph phage isolates and seven lytic Psa phage isolates were isolated from soil in Piedmont and Veneto in northern Italy. Genome characterization of fifteen selected phages revealed that the isolated Pph phages were highly similar and could be considered as isolates of a novel species, whereas the isolated Psa phages grouped into four distinct clades, two of which represent putative novel species. No lysogeny-, virulence- or toxin-related genes were found in four phages, making them suitable for potential biocontrol purposes. A partial biological characterization including a host range analysis was performed on a representative subset of these isolates. This analysis was a prerequisite to assess their efficacy in greenhouse and in field trials, using different delivery strategies.
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Affiliation(s)
- Gabriele Martino
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Dominique Holtappels
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
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Colombi E, Perry BJ, Sullivan JT, Bekuma AA, Terpolilli JJ, Ronson CW, Ramsay JP. Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium. Microb Genom 2021; 7. [PMID: 34605762 PMCID: PMC8627217 DOI: 10.1099/mgen.0.000657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSymAA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSymR7A, with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSymR7A.
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Affiliation(s)
- Elena Colombi
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Benjamin J Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Amanuel A Bekuma
- Centre for Rhizobium Studies, Food Futures Institute, Murdoch University, Perth, WA, Australia, Murdoch University, Perth, WA, Australia.,Present address: Western Australian Department of Primary Industries and Regional Development, Research and Industry Innovation, South Perth, WA, Australia
| | - Jason J Terpolilli
- Centre for Rhizobium Studies, Food Futures Institute, Murdoch University, Perth, WA, Australia, Murdoch University, Perth, WA, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Joshua P Ramsay
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
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Remus-Emsermann MNP, Aicher D, Pelludat C, Gisler P, Drissner D. Conjugation Dynamics of Self-Transmissible and Mobilisable Plasmids into E. coli O157:H7 on Arabidopsis thaliana Rosettes. Antibiotics (Basel) 2021; 10:antibiotics10080928. [PMID: 34438978 PMCID: PMC8388966 DOI: 10.3390/antibiotics10080928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 01/01/2023] Open
Abstract
Many antibiotic resistance genes present in human pathogenic bacteria are believed to originate from environmental bacteria. Conjugation of antibiotic resistance conferring plasmids is considered to be one of the major reasons for the increasing prevalence of antibiotic resistances. A hotspot for plasmid-based horizontal gene transfer is the phyllosphere, i.e., the surfaces of aboveground plant parts. Bacteria in the phyllosphere might serve as intermediate hosts with transfer capability to human pathogenic bacteria. In this study, the exchange of mobilisable and self-transmissible plasmids via conjugation was evaluated. The conjugation from the laboratory strain Escherichia coli S17-1, the model phyllosphere coloniser Pantoea eucalypti 299R, and the model pathogen E. coli O157:H7 to the recipient strain E. coli O157:H7::MRE103 (EcO157:H7red) in the phyllosphere of Arabidopsis thaliana was determined. The results suggest that short-term occurrence of a competent donor is sufficient to fix plasmids in a recipient population of E. coli O157:H7red. The spread of self-transmissible plasmids was limited after initial steep increases of transconjugants that contributed up to 10% of the total recipient population. The here-presented data of plasmid transfer will be important for future modelling approaches to estimate environmental spread of antibiotic resistance in agricultural production environments.
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Affiliation(s)
- Mitja N. P. Remus-Emsermann
- Microbiology of Plant Foods, Agroscope, 8820 Waedenswil, Switzerland;
- School of Biological Sciences, University of Canterbury, Christchurch 8053, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8053, New Zealand
- Institute of Biology-Microbiology, Freie Universität Berlin, 14195 Berlin, Germany
- Correspondence: (M.N.P.R.-E.); (D.D.); Tel.: +49-3083-85-8031 (M.N.P.R.-E.); +49-7571-732-8278 (D.D.)
| | - David Aicher
- Department of Life Sciences, Albstadt-Sigmaringen University, 72488 Sigmaringen, Germany;
| | - Cosima Pelludat
- Plant Pathology and Zoology in Fruit and Vegetable Production, Agroscope, 8820 Waedenswil, Switzerland;
| | - Pascal Gisler
- Microbiology of Plant Foods, Agroscope, 8820 Waedenswil, Switzerland;
| | - David Drissner
- Microbiology of Plant Foods, Agroscope, 8820 Waedenswil, Switzerland;
- Department of Life Sciences, Albstadt-Sigmaringen University, 72488 Sigmaringen, Germany;
- Correspondence: (M.N.P.R.-E.); (D.D.); Tel.: +49-3083-85-8031 (M.N.P.R.-E.); +49-7571-732-8278 (D.D.)
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32
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Mariz-Ponte N, Regalado L, Gimranov E, Tassi N, Moura L, Gomes P, Tavares F, Santos C, Teixeira C. A Synergic Potential of Antimicrobial Peptides against Pseudomonas syringae pv. actinidiae. Molecules 2021; 26:molecules26051461. [PMID: 33800273 PMCID: PMC7962642 DOI: 10.3390/molecules26051461] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is the pathogenic agent responsible for the bacterial canker of kiwifruit (BCK) leading to major losses in kiwifruit productions. No effective treatments and measures have yet been found to control this disease. Despite antimicrobial peptides (AMPs) having been successfully used for the control of several pathogenic bacteria, few studies have focused on the use of AMPs against Psa. In this study, the potential of six AMPs (BP100, RW-BP100, CA-M, 3.1, D4E1, and Dhvar-5) to control Psa was investigated. The minimal inhibitory and bactericidal concentrations (MIC and MBC) were determined and membrane damaging capacity was evaluated by flow cytometry analysis. Among the tested AMPs, the higher inhibitory and bactericidal capacity was observed for BP100 and CA-M with MIC of 3.4 and 3.4-6.2 µM, respectively and MBC 3.4-10 µM for both. Flow cytometry assays suggested a faster membrane permeation for peptide 3.1, in comparison with the other AMPs studied. Peptide mixtures were also tested, disclosing the high efficiency of BP100:3.1 at low concentration to reduce Psa viability. These results highlight the potential interest of AMP mixtures against Psa, and 3.1 as an antimicrobial molecule that can improve other treatments in synergic action.
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Affiliation(s)
- Nuno Mariz-Ponte
- Biology Department, Faculty of Science, University of Porto (FCUP), 4169-007 Porto, Portugal; (L.R.); (E.G.); (F.T.); (C.S.)
- LAQV-REQUIMTE, Biology Department, Faculty of Science (FCUP), University of Porto, 4169-007 Porto, Portugal
- CIBIO—Research Centre in Biodiversity and Genetic Resources, In-BIO-Associate Laboratory, Microbial Diversity and Evolution Group, University of Porto (UP), 4485-661 Vairão, Portugal
- Correspondence:
| | - Laura Regalado
- Biology Department, Faculty of Science, University of Porto (FCUP), 4169-007 Porto, Portugal; (L.R.); (E.G.); (F.T.); (C.S.)
- LAQV-REQUIMTE, Biology Department, Faculty of Science (FCUP), University of Porto, 4169-007 Porto, Portugal
| | - Emil Gimranov
- Biology Department, Faculty of Science, University of Porto (FCUP), 4169-007 Porto, Portugal; (L.R.); (E.G.); (F.T.); (C.S.)
- LAQV-REQUIMTE, Biology Department, Faculty of Science (FCUP), University of Porto, 4169-007 Porto, Portugal
| | - Natália Tassi
- LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences (FCUP), University of Porto, 4169-007 Porto, Portugal; (N.T.); (P.G.); (C.T.)
| | - Luísa Moura
- CISAS—Centre for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, 4900-347 Viana do Castelo, Portugal;
| | - Paula Gomes
- LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences (FCUP), University of Porto, 4169-007 Porto, Portugal; (N.T.); (P.G.); (C.T.)
| | - Fernando Tavares
- Biology Department, Faculty of Science, University of Porto (FCUP), 4169-007 Porto, Portugal; (L.R.); (E.G.); (F.T.); (C.S.)
- CIBIO—Research Centre in Biodiversity and Genetic Resources, In-BIO-Associate Laboratory, Microbial Diversity and Evolution Group, University of Porto (UP), 4485-661 Vairão, Portugal
| | - Conceição Santos
- Biology Department, Faculty of Science, University of Porto (FCUP), 4169-007 Porto, Portugal; (L.R.); (E.G.); (F.T.); (C.S.)
- LAQV-REQUIMTE, Biology Department, Faculty of Science (FCUP), University of Porto, 4169-007 Porto, Portugal
| | - Cátia Teixeira
- LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences (FCUP), University of Porto, 4169-007 Porto, Portugal; (N.T.); (P.G.); (C.T.)
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A Large Tn7-like Transposon Confers Hyper-Resistance to Copper in Pseudomonas syringae pv. syringae. Appl Environ Microbiol 2021; 87:AEM.02528-20. [PMID: 33361370 PMCID: PMC8090865 DOI: 10.1128/aem.02528-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Copper resistance mechanisms provide an important adaptive advantage to plant pathogenic bacteria under exposure to copper treatments. Copper resistance determinants have been described in Pseudomonas syringae pv. syringae (Pss) strains isolated from mango intimately associated with 62 kb plasmids belonging to the pPT23A family (PFP). It has been previously described that the indiscriminate use of copper-based compounds promotes the selection of copper resistant bacterial strains and constitutes a selective pressure in the evolution of copper resistance determinants. Hence, we have explored in this study the copper resistance evolution and the distribution of specific genetic determinants in two different Pss mango populations isolated from the same geographical regions, mainly from southern Spain with an average of 20 years of difference. The total content of plasmids, in particular the 62 kb plasmids, and the number of copper resistant Pss strains were maintained at similar levels over the time. Interestingly, the phylogenetic analysis indicated the presence of a phylogenetic subgroup (PSG) in the Pss mango phylotype, mostly composed of the recent Pss population analyzed in this study that was strongly associated with a hyper-resistant phenotype to copper. Genome sequencing of two selected Pss strains from this PSG revealed the presence of a large Tn7-like transposon of chromosomal location, which harbored putative copper and arsenic resistance genes (COARS Tn7-like). Transformation of the copper sensitive Pss UMAF0158 strain with some putative copper resistance genes and RT-qPCR experiments brought into light the role of COARS Tn7-like transposon in the hyper-resistant phenotype to copper in Pss.IMPORTANCECopper compounds have traditionally been used as standard bactericides in agriculture in the past few decades. However, the extensive use of copper has fostered the evolution of bacterial copper resistance mechanisms. Pseudomonas syringae is a plant pathogenic bacterium used worldwide as a model to study plant-pathogen interactions. The adaption of P. syringae to plant surface environment is the most important step prior to an infection. In this scenario, copper resistance mechanisms could play a key role in improving its epiphytic survival. In this work, a novel Tn7-like transposon of chromosomal location was detected in P. syringae pv. syringae strains isolated from mango. This transposon conferred the highest resistance to copper sulfate described to date for this bacterial phytopathogen. Understanding in depth the copper resistance mechanisms and their evolution are important steps to the agricultural industry to get a better improvement of disease management strategies.
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34
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Abstract
Population genomics is transforming our understanding of pathogen biology and evolution, and contributing to the prevention and management of disease in diverse crops. We provide an overview of key methods in bacterial population genomics and describe recent work focusing on three topics of critical importance to plant pathology: (i) resolving pathogen origins and transmission pathways during outbreak events, (ii) identifying the genetic basis of host specificity and virulence, and (iii) understanding how pathogens evolve in response to changing agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Christina Straub
- Institute of Environmental Science and Research, Health and Environment, Auckland, New Zealand
- Genomics Aotearoa, New Zealand
| | - Elena Colombi
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, Western Australia, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
| | - Honour C McCann
- New Zealand Institute for Advanced Study, Massey University, Albany, New Zealand
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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35
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Webster J, Bogema D, Chapman TA. Comparative Genomics of Xanthomonas citri pv. citri A* Pathotype Reveals Three Distinct Clades with Varying Plasmid Distribution. Microorganisms 2020; 8:microorganisms8121947. [PMID: 33302542 PMCID: PMC7764509 DOI: 10.3390/microorganisms8121947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/23/2022] Open
Abstract
Citrus bacterial canker (CBC) is an important disease of citrus cultivars worldwide that causes blister-like lesions on host plants and leads to more severe symptoms such as plant defoliation and premature fruit drop. The causative agent, Xanthomonas citri pv. citri, exists as three pathotypes—A, A*, and Aw—which differ in their host range and elicited host response. To date, comparative analyses have been hampered by the lack of closed genomes for the A* pathotype. In this study, we sequenced and assembled six CBC isolates of pathotype A* using second- and third-generation sequencing technologies to produce complete, closed assemblies. Analysis of these genomes and reference A, A*, and Aw sequences revealed genetic groups within the A* pathotype. Investigation of accessory genomes revealed virulence factors, including type IV secretion systems and heavy metal resistance genes, differentiating the genetic groups. Genomic comparisons of closed genome assemblies also provided plasmid distribution information for the three genetic groups of A*. The genomes presented here complement existing closed genomes of A and Aw pathotypes that are publicly available and open opportunities to investigate the evolution of X. citri pv. citri and the virulence factors that contribute to this serious pathogen.
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36
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Jayaraman J, Yoon M, Applegate ER, Stroud EA, Templeton MD. AvrE1 and HopR1 from Pseudomonas syringae pv. actinidiae are additively required for full virulence on kiwifruit. MOLECULAR PLANT PATHOLOGY 2020; 21:1467-1480. [PMID: 32969167 PMCID: PMC7548996 DOI: 10.1111/mpp.12989] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/01/2023]
Abstract
Pseudomonas syringae pv. actinidiae ICMP 18884 biovar 3 (Psa3) produces necrotic lesions during infection of its kiwifruit host. Bacterial growth in planta and lesion formation are dependent upon a functional type III secretion system (T3S), which translocates multiple effector proteins into host cells. Associated with the T3S locus is the conserved effector locus (CEL), which has been characterized and shown to be essential for the full virulence in other P. syringae pathovars. Two effectors at the CEL, hopM1 and avrE1, as well as an avrE1-related non-CEL effector, hopR1, have been shown to be redundant in the model pathogen P. syringae pv. tomato DC3000 (Pto), a close relative of Psa. However, it is not known whether CEL-related effectors are required for Psa pathogenicity. The Psa3 allele of hopM1, and its associated chaperone, shcM, have diverged significantly from their orthologs in Pto. Furthermore, the CEL effector hopAA1-1, as well as a related non-CEL effector, hopAA1-2, have both been pseudogenized. We have shown that HopM1 does not contribute to Psa3 virulence due to a truncation in shcM, a truncation conserved in the Psa lineage, probably due to the need to evade HopM1-triggered immunity in kiwifruit. We characterized the virulence contribution of CEL and related effectors in Psa3 and found that only avrE1 and hopR1, additively, are required for in planta growth and lesion production. This is unlike the redundancy described for these effectors in Pto and indicates that these two Psa3 genes are key determinants essential for kiwifruit bacterial canker disease.
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Affiliation(s)
- Jay Jayaraman
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- Bio‐Protection Research CentreLincolnNew Zealand
| | - Minsoo Yoon
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
| | - Emma R. Applegate
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
- Present address:
AgResearch Ltd., Grasslands Research CentrePalmerston NorthNew Zealand
| | - Erin A. Stroud
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- Bio‐Protection Research CentreLincolnNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
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Sieiro C, Areal-Hermida L, Pichardo-Gallardo Á, Almuiña-González R, de Miguel T, Sánchez S, Sánchez-Pérez Á, Villa TG. A Hundred Years of Bacteriophages: Can Phages Replace Antibiotics in Agriculture and Aquaculture? Antibiotics (Basel) 2020; 9:E493. [PMID: 32784768 PMCID: PMC7460141 DOI: 10.3390/antibiotics9080493] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
Agriculture, together with aquaculture, supplies most of the foodstuffs required by the world human population to survive. Hence, bacterial diseases affecting either agricultural crops, fish, or shellfish not only cause large economic losses to producers but can even create food shortages, resulting in malnutrition, or even famine, in vulnerable populations. Years of antibiotic use in the prevention and the treatment of these infections have greatly contributed to the emergence and the proliferation of multidrug-resistant bacteria. This review addresses the urgent need for alternative strategies for the use of antibiotics, focusing on the use of bacteriophages (phages) as biocontrol agents. Phages are viruses that specifically infect bacteria; they are highly host-specific and represent an environmentally-friendly alternative to antibiotics to control and kill pathogenic bacteria. The information evaluated here highlights the effectiveness of phages in the control of numerous major pathogens that affect both agriculture and aquaculture, with special emphasis on scientific and technological aspects still requiring further development to establish phagotherapy as a real universal alternative to antibiotic treatment.
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Affiliation(s)
- Carmen Sieiro
- Department of Functional Biology and Health Sciences, Microbiology Area, University of Vigo, Lagoas-Marcosende, 36310 Vigo, Spain; (L.A.-H.); (Á.P.-G.); (R.A.-G.)
| | - Lara Areal-Hermida
- Department of Functional Biology and Health Sciences, Microbiology Area, University of Vigo, Lagoas-Marcosende, 36310 Vigo, Spain; (L.A.-H.); (Á.P.-G.); (R.A.-G.)
| | - Ángeles Pichardo-Gallardo
- Department of Functional Biology and Health Sciences, Microbiology Area, University of Vigo, Lagoas-Marcosende, 36310 Vigo, Spain; (L.A.-H.); (Á.P.-G.); (R.A.-G.)
| | - Raquel Almuiña-González
- Department of Functional Biology and Health Sciences, Microbiology Area, University of Vigo, Lagoas-Marcosende, 36310 Vigo, Spain; (L.A.-H.); (Á.P.-G.); (R.A.-G.)
| | - Trinidad de Miguel
- Department of Microbiology and Parasitology, University of Santiago de Compostela, 5706 Santiago de Compostela, Spain; (T.d.M.); (S.S.)
| | - Sandra Sánchez
- Department of Microbiology and Parasitology, University of Santiago de Compostela, 5706 Santiago de Compostela, Spain; (T.d.M.); (S.S.)
| | - Ángeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydnay NSN 2006, Australia;
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, University of Santiago de Compostela, 5706 Santiago de Compostela, Spain; (T.d.M.); (S.S.)
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McCann HC. Skirmish or war: the emergence of agricultural plant pathogens. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:147-152. [PMID: 32712539 DOI: 10.1016/j.pbi.2020.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Understanding the ecological and evolutionary processes underlying the emergence of infectious disease is critically important in guiding prevention, management and breeding strategies. Novel pathogen lineages may arise within agricultural environments, wild hosts or from non-host associated disease reservoirs. Although the source of most disease outbreaks remains unknown, environmental and zoonotic origins are frequently identified in mammalian pathosystems and expanded sampling of plant pathosystems reveals important links with wild populations. This review describes key ecological and evolutionary processes underlying disease emergence, with particular emphasis on shifts from wild reservoirs to cultivated hosts and genetic mechanisms driving host adaption subsequent to emergence.
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Affiliation(s)
- Honour C McCann
- New Zealand Institute for Advanced Study, Massey University, Albany, New Zealand; Max Planck Institute for Developmental Biology, Tübingen, Germany.
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Characterization of Bacteriophages against Pseudomonas Syringae pv. Actinidiae with Potential Use as Natural Antimicrobials in Kiwifruit Plants. Microorganisms 2020; 8:microorganisms8070974. [PMID: 32610695 PMCID: PMC7409275 DOI: 10.3390/microorganisms8070974] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of a bacterial canker in kiwifruit plants and has caused economic losses worldwide. Currently, the primary strategies to control this pathogen include the use of copper-based compounds and even antibiotics. However, the emergence of isolates of Psa that are resistant to these agrochemicals has raised the need for new alternatives to control this pathogen. Bacteriophages have been proposed as an alternative to control bacterial infections in agriculture, including Psa. Here, we show the isolation and characterization of 13 phages with the potential to control Psa infections in kiwifruit plants. The phages were characterized according to their host range and restriction fragment length polymorphism (RFLP) pattern. Four phages were selected according to their lytic effect on the bacteria and their tolerance to different environmental conditions of pH (4–7), temperature (4–37 °C), and solar radiation exposure (30 and 60 min). The selected phages (CHF1, CHF7, CHF19, and CHF21) were sequenced, revealing a high identity with the podophage of Psa phiPSA2. In vitro assays with kiwifruit leaf samples demonstrated that the mixture of phages reduced the Psa bacterial load within three hours post-application and was able to reduce the damage index in 50% of cases. Similarly, assays with kiwifruit plants maintained in greenhouse conditions showed that these phages were able to reduce the Psa bacterial load in more than 50% of cases and produced a significant decrease in the damage index of treated plants after 30 days. Finally, none of the selected phages were able to infect the other bacteria present in the natural microbiota of kiwifruit plants. These results show that bacteriophages are an attractive alternative to control Psa infections in kiwifruit plants.
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40
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Botelho J, Schulenburg H. The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution. Trends Microbiol 2020; 29:8-18. [PMID: 32536522 DOI: 10.1016/j.tim.2020.05.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
Mobile genetic elements (MGEs), such as plasmids and integrative and conjugative elements (ICEs), are main drivers for the spread of antibiotic resistance (AR). Coevolution between bacteria and plasmids shapes the transfer and stability of plasmids across bacteria. Although ICEs outnumber conjugative plasmids, the dynamics of ICE-bacterium coevolution, ICE transfer rates, and fitness costs are as yet largely unexplored. Conjugative plasmids and ICEs are both transferred by type IV secretion systems, but ICEs are typically immune to segregational loss, suggesting that the evolution of ICE-bacterium associations varies from that of plasmid-bacterium associations. Considering the high abundance of ICEs among bacteria, ICE-bacterium dynamics represent a promising challenge for future research that will enhance our understanding of AR spread in human pathogens.
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Affiliation(s)
- João Botelho
- Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany.
| | - Hinrich Schulenburg
- Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
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41
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Liu T, Li L, Wei W, Wang K, Yang Q, Wang E. Yersinia ruckeri strain SC09 disrupts proinflammatory activation via Toll/IL-1 receptor-containing protein STIR-3. FISH & SHELLFISH IMMUNOLOGY 2020; 99:424-434. [PMID: 32087278 DOI: 10.1016/j.fsi.2020.02.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/11/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
Virulent pathogenic microorganisms often enhance their infectivity through immune evasion mechanisms. Our research on the integrative and conjugative element (ICE(r2)) of the virulent fish pathogen Yersinia ruckeri SC09 led to the identification of genes related to immune evasion (designated stir-1, stir-2, stir-3 and stir-4), among which stir-1 and stir-2 were determined as the key contributors to bacterial toxicity and immune evasion. Here, we further examined the ability of stir-3 to mediate immune evasion based on detailed bioinformatic analysis of ICE(r2) from Y. ruckeri SC09. Interactions among the translated STIR-1, STIR-2, STIR-3 and STIR-4 proteins in the secretory process were additionally explored. STIR-3 was positively correlated with bacterial toxicity and inhibited host toll-like receptor (TLR) signaling by interacting with MyD88, thereby facilitating bacterial survival in host cells. Importantly, our data showed co-secretion of STIR-1, STIR-2 and STIR-3 as a complex, with secretion failure occurring in the absence of any one of these proteins. While stir-1, stir-2, stir-3 and stir-4 genes werespecific to Y. ruckeri SC09, the ICE(r2) region where these genes were located is a mobile component widely distributed in bacteria. Therefore, the potential transmission risk of these immune evasion genes requires further research attention.
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Affiliation(s)
- Tao Liu
- Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Liangyu Li
- Institute of Fisheries of Chengdu Agriculture and Forestry Academy, Chengdu, China
| | - Wenyan Wei
- Institute of Fisheries of Chengdu Agriculture and Forestry Academy, Chengdu, China
| | - Kaiyu Wang
- Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Qian Yang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Erlong Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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Quistad SD, Doulcier G, Rainey PB. Experimental manipulation of selfish genetic elements links genes to microbial community function. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190681. [PMID: 32200751 PMCID: PMC7133536 DOI: 10.1098/rstb.2019.0681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
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Affiliation(s)
- Steven D Quistad
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France
| | - Guilhem Doulcier
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France
| | - Paul B Rainey
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
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Ho J, Zhao M, Wojcik S, Taiaroa G, Butler M, Poulter R. The application of the CRISPR–Cas9 system in Pseudomonas syringae pv. actinidiae. J Med Microbiol 2020; 69:478-486. [DOI: 10.1099/jmm.0.001124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Introduction.Pseudomonas syringaepv. actinidiae (Psa) has emerged as a major bacterial pathogen of kiwifruit cultivation throughout the world.Aim.We aim to introduce a CRISPR–Cas9 system, a commonly used genome editing tool, into Psa. The protocols may also be useful in otherPseudomonasspecies.Methodology.Using standard molecular biology techniques, we modified plasmid pCas9, which carries the CRISPR–Cas9 sequences fromStreptococcus pyogenes,for use in Psa. The final plasmid, pJH1, was produced in a series of steps and is maintained with selection in bothEscherichia coliand Psa.Results.We have constructed plasmids carrying a CRISPR–Cas9 system based on that ofS. pyogenes, which can be maintained, under selection, in Psa. We have shown that the gene targeting capacity of the CRISPR–Cas9 system is active and that the Cas9 protein is able to cleave the targeted sites. The Cas9 was directed to several different sites in theP. syringaegenome. Using Cas9 we have generated Psa transformants that no longer carry the native plasmid present in Psa, and other transformants that lack the integrative, conjugative element, Pac_ICE1. Targeting of a specific gene, a chromosomal non-ribosomal peptide synthetase, led to gene knockouts with the transformants having deletions encompassing the target site.Conclusion.We have constructed shuttle plasmids carrying a CRISPR–Cas9 system that are maintained in bothE. coliandP. syringaepv. actinidiae. We have used this gene editing system to eliminate features of the accessory genome (plasmids or ICEs) from Psa and to target a single chromosomal gene.
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Affiliation(s)
- Joycelyn Ho
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Min Zhao
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Samuel Wojcik
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - George Taiaroa
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Margi Butler
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Russell Poulter
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Kim MJ, Chae DH, Cho G, Kim DR, Kwak YS. Characterization of Antibacterial Strains against Kiwifruit Bacterial Canker Pathogen. THE PLANT PATHOLOGY JOURNAL 2019; 35:473-485. [PMID: 31632222 PMCID: PMC6788412 DOI: 10.5423/ppj.oa.05.2019.0154] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/09/2019] [Accepted: 07/22/2019] [Indexed: 06/02/2023]
Abstract
Kiwifruit (Actinidia spp.) is an economically important crop and a bacterial canker disease, caused by Pseudomonas syringae pv. actinidiae (Psa), is the most destructive disease in kiwifruit production. Therefore, prevent and control of the disease is a critical issue in kiwifruit industry worldwide. Unfortunately, there is no reliable control methods have been developed. Recently, interest in disease control using microbial agents is growing. However, kiwifruit microbiota and their roles in the disease control is mainly remaining unknown. In this study, we secured bacterial libraries from kiwifruit ecospheres (rhizosphere, endospere, and phyllosphere) and screened reliable biocontrol strains against Psa. As the results, Streptomyces racemochromogenes W1SF4, Streptomyces sp. W3SF9 and S. parvulus KPB2 were selected as anti-Psa agents from the libraries. The strains showed forcible antibacterial activity as well as exceptional colonization ability on rhizosphere or phyllosphere of kiwifruit. Genome analyses of the strains suggested that the strains may produce several anti-Psa secondary metabolites. Our results will contribute to develop biocontrol strains against the kiwifruit canker pathogen and the disease management strategies.
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Affiliation(s)
- Min-Jung Kim
- Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828,
Korea
| | - Dae-Han Chae
- Division of Applied Life Science, Gyeongsang National University, Jinju 58282,
Korea
| | - Gyeongjun Cho
- Division of Applied Life Science, Gyeongsang National University, Jinju 58282,
Korea
| | - Da-Ran Kim
- Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828,
Korea
| | - Youn-Sig Kwak
- Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828,
Korea
- Division of Applied Life Science, Gyeongsang National University, Jinju 58282,
Korea
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Integrated Use of Aureobasidium pullulans Strain CG163 and Acibenzolar-S-Methyl for Management of Bacterial Canker in Kiwifruit. PLANTS 2019; 8:plants8080287. [PMID: 31443158 PMCID: PMC6724088 DOI: 10.3390/plants8080287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/02/2019] [Accepted: 08/12/2019] [Indexed: 11/21/2022]
Abstract
An isolate of Aureobasidium pullulans (strain = CG163) and the plant defence elicitor acibenzolar-S-methyl (ASM) were investigated for their ability to control leaf spot in kiwifruit caused by Pseudomonassyringae pv. actinidiae biovar 3 (Psa). Clonal Actinidia chinensis var. deliciosa plantlets (‘Hayward’) were treated with ASM, CG163 or ASM + CG163 at seven and one day before inoculation with Psa. ASM (0.2 g/L) was applied either as a root or foliar treatments and CG163 was applied as a foliar spray containing 2 × 107 CFU/mL. Leaf spot incidence was significantly reduced by all treatments compared with the control. The combination of ASM + CG163 had greater efficacy (75%) than either ASM (55%) or CG163 (40%) alone. Moreover, treatment efficacy correlated positively with the expression of defence-related genes: pathogenesis-related protein 1 (PR1), β-1,3-glucosidase, Glucan endo 1,3-β-glucosidase (Gluc_PrimerH) and Class IV chitinase (ClassIV_Chit), with greater gene upregulation in plants treated with ASM + CG163 than by the individual treatments. Pathogen population studies indicated that CG163 had significant suppressive activity against epiphytic populations of Psa. Endophytic populations were reduced by ASM + CG163 but not by the individual treatments, and by 96–144 h after inoculation were significantly lower than the control. Together these data suggest that ASM + CG163 have complementary modes of action that contribute to greater control of leaf spotting than either treatment alone.
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Wang F, Li J, Ye K, Liu P, Gong H, Jiang Q, Qi B, Mo Q. An in vitro Actinidia Bioassay to Evaluate the Resistance to Pseudomonas syringae pv. actinidiae. THE PLANT PATHOLOGY JOURNAL 2019; 35:372-380. [PMID: 31481860 PMCID: PMC6706018 DOI: 10.5423/ppj.oa.02.2019.0035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/15/2019] [Accepted: 05/19/2019] [Indexed: 06/10/2023]
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is by far the most important pathogen of kiwifruit. Sustainable expansion of the kiwifruit industry requires the use of Psa-tolerant or resistant genotypes for the breeding of tolerant cultivars. However, the resistance of most existing kiwifruit cultivars and wild genotypes is poorly understood, and suitable evaluation methods of Psa resistance in Actinidia have not been established. A unique in vitro method to evaluate Psa resistance has been developed with 18 selected Actinidia genotypes. The assay involved debarking and measuring the lesions of cane pieces inoculated with the bacterium in combination with the observation of symptoms such as callus formation, sprouting of buds, and the extent to which Psa invaded xylem. Relative Psa resistance or tolerance was divided into four categories. The division results were consistent with field observations. This is the first report of an in vitro assay capable of large-scale screening of Psa-resistance in Actinidia germplasm with high accuracy and reproducibility. The assay would considerably facilitate the breeding of Psa-resistant cultivars and provide a valuable reference and inspiration for the resistance evaluation of other plants to different pathogens.
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Affiliation(s)
| | | | | | | | | | | | | | - Quanhui Mo
- Corresponding author: Phone) (+86)773-3550103, FAX) (+86)773-3550067, E-mail)
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Kering KK, Kibii BJ, Wei H. Biocontrol of phytobacteria with bacteriophage cocktails. PEST MANAGEMENT SCIENCE 2019; 75:1775-1781. [PMID: 30624034 DOI: 10.1002/ps.5324] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/01/2019] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Crop loss due to plant pathogens has provoked renewed interest in bacteriophages as a feasible biocontrol strategy of plant diseases. Phage cocktails in particular present a viable option for broadening the phage host range, limiting the emergence of bacterial resistance while maintaining the lytic activity of the phages. It is therefore important that the design used to formulate a phage cocktail should result in the most effective cocktail against the pathogen. It is also critical that certain factors are considered during the formulation and application of a phage cocktail: their stability, the production time and cost of complex cocktails, the potential impact on untargeted bacteria, the timing of phage application, and the persistence in the plant environment. Continuous monitoring is required to ensure that the efficacy of a cocktail is sustained due to the dynamic nature of phages. Although phage cocktails are considered as a plausible biocontrol strategy of phytobacteria, more research needs to be done to understand the complex interaction between phages and bacteria in the plant environment, and to overcome the technical obstacles. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Kelvin K Kering
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Belindah J Kibii
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
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Zhao Z, Chen J, Gao X, Zhang D, Zhang J, Wen J, Qin H, Guo M, Huang L. Comparative genomics reveal pathogenicity-related loci in Pseudomonas syringae pv. actinidiae biovar 3. MOLECULAR PLANT PATHOLOGY 2019; 20:923-942. [PMID: 31025813 PMCID: PMC6589868 DOI: 10.1111/mpp.12803] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bacterial canker of kiwifruit, is a severe global disease caused by Pseudomonas syringae pv. actinidiae (Psa). Here, we found that Psa biovar 3 (Psa3) was the only biovar consisting of three widely distributed clades in the largest Chinese kiwifruit cultivated area. Comparative genomics between the three clades revealed 13 polymorphic genes, each of which had multiple intra-clade variations. For instance, we confirmed that the polymorphic copA gene, which encodes a periplasmic protein CopA that is translocated by the Twin-arginine targeting (Tat) system, was involved in copper tolerance. We also found extensive variation in pathogenicity amongst strains within each genetically monomorphic clade. Accordingly, the pathogenic determinants of Psa3 were identified via a genomic comparison of phenotypically different strains within each clade. A case study of the high- and low-virulence strains in the clade 2 of Psa3 revealed that an hfq variant involved in in vitro growth and virulence, while a conserved locus 930 bp upstream of the hrpR gene in the Type III secretion system (T3SS) cluster was required for full pathogenicity on kiwifruit and elicitation of the hypersensitivity response on non-host Nicotiana benthamiana. The '-930' locus is involved in transcriptional regulation of hrpR/S and modulates T3SS function via the hierarchical 'HrpR/S-HrpL-T3SS/effector' regulatory cascade in Psa. Our results provide insights into the molecular basis underlying the genetic diversification and evolution of pathogenicity in Psa3 since kiwifruit canker emerged in China in the 1980s.
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Affiliation(s)
- Zhibo Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas; and College of Plant ProtectionNorthwest A&F UniversityYangling712100P. R. China
| | - Jiliang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas; and College of Plant ProtectionNorthwest A&F UniversityYangling712100P. R. China
| | - Xiaoning Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas; and College of Plant ProtectionNorthwest A&F UniversityYangling712100P. R. China
| | - Di Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas; and College of Plant ProtectionNorthwest A&F UniversityYangling712100P. R. China
| | - Jinlong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas; and College of Plant ProtectionNorthwest A&F UniversityYangling712100P. R. China
| | - Jing Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas; and College of Plant ProtectionNorthwest A&F UniversityYangling712100P. R. China
| | - Huqiang Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas; and College of Plant ProtectionNorthwest A&F UniversityYangling712100P. R. China
| | - Ming Guo
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu ProvinceJiangsu Normal UniversityNo. 101 Shanghai RdTongshan DistrictXuzhou221116P. R. China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas; and College of Plant ProtectionNorthwest A&F UniversityYangling712100P. R. China
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In Silico Identification of Three Types of Integrative and Conjugative Elements in Elizabethkingia anophelis Strains Isolated from around the World. mSphere 2019; 4:4/2/e00040-19. [PMID: 30944210 PMCID: PMC6449604 DOI: 10.1128/msphere.00040-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Elizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE. Elizabethkingia anophelis is an emerging global multidrug-resistant opportunistic pathogen. We assessed the diversity among 13 complete genomes and 23 draft genomes of E. anophelis strains derived from various environmental settings and human infections from different geographic regions around the world from 1950s to the present. Putative integrative and conjugative elements (ICEs) were identified in 31/36 (86.1%) strains in the study. A total of 52 putative ICEs (including eight degenerated elements lacking integrases) were identified and categorized into three types based on the architecture of the conjugation module and the phylogeny of the relaxase, coupling protein, TraG, and TraJ protein sequences. The type II and III ICEs were found to integrate adjacent to tRNA genes, while type I ICEs integrate into intergenic regions or into a gene. The ICEs carry various cargo genes, including transcription regulator genes and genes conferring antibiotic resistance. The adaptive immune CRISPR-Cas system was found in nine strains, including five strains in which CRISPR-Cas machinery and ICEs coexist at different locations on the same chromosome. One ICE-derived spacer was present in the CRISPR locus in one strain. ICE distribution in the strains showed no geographic or temporal patterns. The ICEs in E. anophelis differ in architecture and sequence from CTnDOT, a well-studied ICE prevalent in Bacteroides spp. The categorization of ICEs will facilitate further investigations of the impact of ICE on virulence, genome epidemiology, and adaptive genomics of E. anophelis. IMPORTANCEElizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE.
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50
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He R, Liu P, Jia B, Xue S, Wang X, Hu J, Al Shoffe Y, Gallipoli L, Mazzaglia A, Balestra GM, Zhu L. Genetic Diversity of Pseudomonas syringae pv. actinidiae Strains from Different Geographic Regions in China. PHYTOPATHOLOGY 2019; 109:347-357. [PMID: 30226424 DOI: 10.1094/phyto-06-18-0188-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Pseudomonas syringae pv. actinidiae causes kiwifruit bacterial canker, with severe infection of the kiwifruit plant resulting in heavy economic losses. Little is known regarding the biodiversity and genetic variation of populations of P. syringae pv. actinidiae in China. A collection of 269 strains of P. syringae pv. actinidiae was identified from 300 isolates obtained from eight sampling sites in five provinces in China. The profiles of 50 strains of P. syringae pv. actinidiae and one strain of P. syringae pv. actinidifoliorum were characterized by Rep-, insertion sequences 50, and randomly amplified polymorphic DNA polymerase chain reaction (PCR). Discriminant analysis of principal coordinates, principal component analysis, and hierarchical cluster analysis were used to analyze the combined fingerprints of the different PCR assays. The results revealed that all isolates belonged to the Psa3 group, that strains of P. syringae pv. actinidiae from China have broad genetic variability that was related to source geographic region, and that Chinese strains can be readily differentiated from strains from France but are very similar to those from Italy. Multilocus sequence typing of 24 representative isolates using the concatenated sequences of five housekeeping genes (cts, gapA, gyrB, pfk, and rpoD) demonstrated that strain Jzhy2 from China formed an independent clade compared with the other biovars, which possessed the hopH1 effector gene but lacked the hopA1 effector gene. A constellation analysis based on the presence or absence of the four loci coding for phytotoxins and a cluster analysis based on the 11 effector genes showed that strains from China formed two distinct clades. All of the strains, including K3 isolated in 1997 from Jeju, Korea, lacked the cfl gene coding for coronatine. In contrast, the tox-argK gene cluster coding for phaseolotoxin was detected in K3 and in the biovar 1 strains (K3, Kw30, and Psa92), and produced a false-positive amplicon for the hopAM1-like gene in this study. To date, only one biovar (biovar 3) is represented by the strains of P. syringae pv. actinidiae from China, despite China being the center of origin for kiwifruit.
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Affiliation(s)
- Rong He
- 1 Key Lab of Pomology, School of Horticulture, Anhui Agricultural University, West Changjiang Road 130, Hefei 230036, Anhui Province, P.R. China
| | - Pu Liu
- 1 Key Lab of Pomology, School of Horticulture, Anhui Agricultural University, West Changjiang Road 130, Hefei 230036, Anhui Province, P.R. China
| | - Bing Jia
- 1 Key Lab of Pomology, School of Horticulture, Anhui Agricultural University, West Changjiang Road 130, Hefei 230036, Anhui Province, P.R. China
| | - Shizhou Xue
- 1 Key Lab of Pomology, School of Horticulture, Anhui Agricultural University, West Changjiang Road 130, Hefei 230036, Anhui Province, P.R. China
| | - Xiaojie Wang
- 1 Key Lab of Pomology, School of Horticulture, Anhui Agricultural University, West Changjiang Road 130, Hefei 230036, Anhui Province, P.R. China
| | - Jiayong Hu
- 1 Key Lab of Pomology, School of Horticulture, Anhui Agricultural University, West Changjiang Road 130, Hefei 230036, Anhui Province, P.R. China
| | - Yosef Al Shoffe
- 2 Section of Horticulture, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA; and
| | - Lorenzo Gallipoli
- 3 Department of Science and Technologies for Agriculture, Forestry, Nature and Energy, University of Tuscia, Via S. Camillo de Lellis 01100, Viterbo, Italy
| | - Angelo Mazzaglia
- 3 Department of Science and Technologies for Agriculture, Forestry, Nature and Energy, University of Tuscia, Via S. Camillo de Lellis 01100, Viterbo, Italy
| | - Giorgio M Balestra
- 3 Department of Science and Technologies for Agriculture, Forestry, Nature and Energy, University of Tuscia, Via S. Camillo de Lellis 01100, Viterbo, Italy
| | - Liwu Zhu
- 1 Key Lab of Pomology, School of Horticulture, Anhui Agricultural University, West Changjiang Road 130, Hefei 230036, Anhui Province, P.R. China
- 2 Section of Horticulture, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA; and
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